PsfR, a factor that stimulates psbAI expression in the cyanobacterium Synechococcus elongatus PCC 7942

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 1031-1040 ◽  
Author(s):  
Colleen Thomas ◽  
Carol R. Andersson ◽  
Shannon R. Canales ◽  
Susan S. Golden
Keyword(s):  
Protein Interactions ◽  
Regulation Of Gene Expression ◽  
D1 Protein ◽  
Direct Interaction ◽  
Synechococcus Elongatus ◽  
Phosphoryl Transfer ◽  
Reaction Centre ◽  
Protein Protein Interactions ◽  
Circadian Expression ◽  
Synechococcus Elongatus Pcc 7942

In this paper a gene (psfR) is reported that regulates psbAI activity in Synechococcus elongatus, a unicellular photoautotrophic cyanobacterium that carries out oxygenic (plant-type) photosynthesis and exhibits global circadian regulation of gene expression. In S. elongatus, a family of three psbA genes encodes the D1 protein of the photosystem II reaction centre. Overexpression of psfR results in increased expression of psbAI, but does not affect the circadian timing of psbAI expression. psfR overexpression affected some, but not all of the genes routinely surveyed for circadian expression. PsfR acts (directly or indirectly) on the psbAI basal promoter region. psfR knockout mutants exhibit wild-type psbAI expression, suggesting that other factors can regulate psbAI expression in the absence of functional PsfR. PsfR contains two receiver-like domains (found in bacterial two-component signal transduction systems), one of which lacks the conserved aspartyl residue required for phosphoryl transfer. PsfR also contains a GGDEF domain. The presence of these domains and the absence of a detectable conserved DNA-binding domain suggest that PsfR may regulate psbAI expression via protein–protein interactions or GGDEF activity (the production of cyclic dinucleotides) rather than direct interaction with the psbAI promoter.

scholarly journals TRIM22. A Multitasking Antiviral Factor

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1864
Author(s):  
Isabel Pagani ◽  
Guido Poli ◽  
Elisa Vicenzi
Keyword(s):  
Protein Interactions ◽  
Influenza A ◽  
Direct Interaction ◽  
Type I Interferons ◽  
Viral Gene ◽  
Target Cells ◽  
Type I ◽  
Protein Protein Interactions ◽  
Viral Genomes ◽  
Dna And Rna

Viral invasion of target cells triggers an immediate intracellular host defense system aimed at preventing further propagation of the virus. Viral genomes or early products of viral replication are sensed by a number of pattern recognition receptors, leading to the synthesis and production of type I interferons (IFNs) that, in turn, activate a cascade of IFN-stimulated genes (ISGs) with antiviral functions. Among these, several members of the tripartite motif (TRIM) family are antiviral executors. This article will focus, in particular, on TRIM22 as an example of a multitarget antiviral member of the TRIM family. The antiviral activities of TRIM22 against different DNA and RNA viruses, particularly human immunodeficiency virus type 1 (HIV-1) and influenza A virus (IAV), will be discussed. TRIM22 restriction of virus replication can involve either direct interaction of TRIM22 E3 ubiquitin ligase activity with viral proteins, or indirect protein–protein interactions resulting in control of viral gene transcription, but also epigenetic effects exerted at the chromatin level.

Identification of a C/EBP-Rel complex in avian lymphoid cells

1994 ◽  
Vol 14 (10) ◽  
pp. 6635-6646
Author(s):  
J A Diehl ◽  
M Hannink
Keyword(s):  
Gene Expression ◽  
Affinity Chromatography ◽  
Protein Interactions ◽  
Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Lymphoid Cells ◽  
Cytokine Gene Expression ◽  
Protein Protein Interactions ◽  
Dna Complex ◽  
Dna Affinity Chromatography

Protein-protein interactions between the CCAAT box enhancer-binding proteins (C/EBP) and the Rel family of transcription factors have been implicated in the regulation of cytokine gene expression. We have used sequence-specific DNA affinity chromatography to purify a complex from avian T cells that binds to a consensus C/EBP motif. Our results provide evidence that Rel-related proteins are components of the C/EBP-DNA complex as a result of protein-protein interactions with the C/EBP proteins. A polyclonal antiserum raised against the Rel homology domain of v-Rel and antisera raised against two human RelA-derived peptides specifically induced a supershift of the C/EBP-DNA complex in mobility shift assays using the affinity-purified C/EBP. In addition, several kappa B-binding proteins copurified with the avian C/EBP complex through two rounds of sequence-specific DNA affinity chromatography. The kappa B-binding proteins are distinct from the C/EBP proteins that directly contact DNA containing the C/EBP binding site. The identification of a protein complex that binds specifically to a consensus C/EBP site and contains both C/EBP and Rel family members suggests a novel mechanism for regulation of gene expression by Rel family proteins.

scholarly journals Characterization of major chromatin assembly proteins in tetrahymena thermophile using proeomic and molecular evolutionary analyses

2021 ◽  
Author(s):  
Syed N Shah
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Regulation Of Gene Expression ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Protein Protein Interactions ◽  
Selective Forces ◽  
Assembly Proteins

Histones H3/H4 are deposited onto DNA in a replication-dependent or independent fashion by the CAF1 and HIRA protein complexes. Despite the identification of these protein complexes, mechanistic details remain unclear. Recently, we showed that in T. thermophila histone chaperones Nrp1, Asf1 and the Impβ6 importin function together to transport newly synthesized H3/H4 from the cytoplasm to the nucleus. To characterize chromatin assembly proteins in T.thermophila, I used affinity purification combined with mass spectrometry to identify protein-protein interactions of Nrp1, Cac2 subunit of CAF1, HIRA and histone modifying Hat1-complex in T. thermophila. I found that the three-subunit T.thermophila CAF1 complex interacts with Casein Kinase 2 (CKII), possibly accounting for previously reported human CAF1phosphorylation. I also found that Hat2 subunit of HAT1 complex is also shared by CAF1 complex as its Cac3 subunit. This suggests that Hat2/Cac3 might exist in two separate pools of protein complexes. Remarkably, proteomic analysis of Hat2/Cac3 in turn revealed that it forms several complexes with other proteins including SIN3, RXT3, LIN9 and TESMIN, all of which have known roles in the regulation of gene expression. Finally, I asked how selective forces might have impacted on the function of proteins involved in H3/H4 transport. Focusing on NASP which possesses several TPR motifs, I showed that its protein-protein interactions are conserved in T. thermophila. Using molecular evolutionary methods I show that different TPRs in NASP evolve at different rates possibly accounting for the functional diversity observed among different family members.

Identification of a new Schistosoma mansoni SMYB1 partner: putative roles in RNA metabolism

Parasitology ◽  
2013 ◽  
Vol 140 (9) ◽  
pp. 1085-1095 ◽  
Author(s):  
ELIZÂNGELA A. ROCHA ◽  
ANALINA F. VALADÃO ◽  
CÍNTIA M. REZENDE ◽  
SILVIA REGINA COSTA DIAS ◽  
ANDRÉA M. MACEDO ◽  
...  
Keyword(s):  
Schistosoma Mansoni ◽  
Protein Interactions ◽  
Regulation Of Gene Expression ◽  
Protein Protein Interactions ◽  
Rna Molecules ◽  
Mrna Metabolism ◽  
Ribonucleoprotein Complexes ◽  
Small Nuclear Ribonucleoprotein ◽  
Life Cycle Stages ◽  
Molecular Events

SUMMARYSMYB1 is a Schistosoma mansoni protein highly similar to members of the Y-box binding protein family. Similar to other homologues, SMYB1 is able to bind double- and single-stranded DNA, as well as RNA molecules. The characterization of proteins involved in the regulation of gene expression in S. mansoni is of great importance for the understanding of molecular events that control morphological and physiological changes in this parasite. Here we demonstrate that SMYB1 is located in the cytoplasm of cells from different life-cycle stages of S. mansoni, suggesting that this protein is probably acting in mRNA metabolism in the cytoplasm and corroborating previous findings from our group that showed its ability to bind RNA. Protein–protein interactions are important events in all biological processes, since most proteins execute their functions through large supramolecular structures. Yeast two-hybrid screenings using SMYB1 as bait identified a partner in S. mansoni similar to the SmD3 protein of Drosophila melanogaster (SmRNP), which is important in the assembly of small nuclear ribonucleoprotein complexes. Also, pull-down assays were conducted using immobilized GST-SMYB1 proteins and confirmed the SMYB1-SmRNP interaction. The interaction of SMYB1 with a protein involved in mRNA processing suggests that it may act in processes such as turnover, transport and stabilization of RNA molecules.

scholarly journals Analysis of the Signaling Activities of Localization Mutants of β-Catenin during Axis Specification in Xenopus

1997 ◽  
Vol 139 (1) ◽  
pp. 229-243 ◽  
Author(s):  
Jeffrey R. Miller ◽  
Randall T. Moon
Keyword(s):  
Cell Fate ◽  
Protein Interactions ◽  
Glycogen Synthase ◽  
Regulation Of Gene Expression ◽  
Unexpected Result ◽  
Protein Protein Interactions ◽  
Cell Fates ◽  
Xenopus Embryos ◽  
Axis Specification ◽  
Dorsal Cell Fate

In Xenopus embryos, β-catenin has been shown to be both necessary and sufficient for the establishment of dorsal cell fates. This signaling activity is thought to depend on the binding of β-catenin to members of the Lef/Tcf family of transcription factors and the regulation of gene expression by this complex. To test whether β-catenin must accumulate in nuclei to establish dorsal cell fate, we constructed various localization mutants that restrict β-catenin to either the plasma membrane, the cytosol, or the nucleus. When overexpressed in Xenopus embryos, the proteins localize as predicted, but surprisingly all forms induce an ectopic axis, indicative of inducing dorsal cell fates. Given this unexpected result, we focused on the membrane-tethered form of β-catenin to resolve the apparent discrepancy between its membrane localization and the hypothesized role of nuclear β-catenin in establishing dorsal cell fate. We demonstrate that overexpression of membrane-tethered β-catenin elevates the level of free endogenous β-catenin, which subsequently accumulates in nuclei. Consistent with the hypothesis that it is this pool of non–membrane-associated β-catenin that signals in the presence of membrane-tethered β-catenin, overexpression of cadherin, which binds free β-catenin, blocks the axis-inducing activity of membrane- tethered β-catenin. The mechanism by which ectopic membrane-tethered β-catenin increases the level of endogenous β-catenin likely involves competition for the adenomatous polyposis coli (APC) protein, which in other systems has been shown to play a role in degradation of β-catenin. Consistent with this hypothesis, membrane-tethered β-catenin coimmunoprecipitates with APC and relocalizes APC to the membrane in cells. Similar results are observed with ectopic plakoglobin, casting doubt on a normal role for plakoglobin in axis specification and indicating that ectopic proteins that interact with APC can artifactually elevate the level of endogenous β-catenin, likely by interfering with its degradation. These results highlight the difficulty in interpreting the activity of an ectopic protein when it is assayed in a background containing the endogenous protein. We next investigated whether the ability of β-catenin to interact with potential protein partners in the cell may normally be regulated by phosphorylation. Compared with nonphosphorylated β-catenin, β-catenin phosphorylated by glycogen synthase kinase-3 preferentially associates with microsomal fractions expressing the cytoplasmic region of N-cadherin. These results suggest that protein–protein interactions of β-catenin can be influenced by its state of phosphorylation, in addition to prior evidence that this phosphorylation modulates the stability of β-catenin.

Functional mapping of Toll/interleukin-1 signalling networks by expression cloning

2005 ◽  
Vol 33 (6) ◽  
pp. 1405-1406 ◽  
Author(s):  
E. Kiss-Toth ◽  
D.H. Wyllie ◽  
K. Holland ◽  
L. Marsden ◽  
V. Jozsa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Interleukin 1 ◽  
Regulation Of Gene Expression ◽  
Expression Cloning ◽  
Functional Screening ◽  
Protein Protein Interactions ◽  
Signalling Network ◽  
Screening Platform ◽  
Inflammatory Signalling

Multiple cellular proteins have been identified as participating in Toll/interleukin-1 receptor-mediated inflammatory gene expression. The continuing isolation of novel components, based on sequence similarities, protein–protein interactions and protein purification, suggests that many elements of this signalling network remain to be identified. We report here the development of a high-throughput functional screening platform and its application for the identification of components of inflammatory signalling networks. Our results enable us to estimate that 100–150 gene products are involved in controlling the transcription of the human interleukin 8 gene. The approach, which is simple and robust, constitutes a general method for mapping signal transduction systems and for rapid isolation of a large number of signalling components based on the control of pathways leading to regulation of gene expression.

Towards an Understanding of Plant Gene Regulation: The Action of Nuclear Factors

1991 ◽  
Vol 46 (1-2) ◽  
pp. 1-11 ◽  
Author(s):  
Kurt Weising ◽  
Günter Kahl
Keyword(s):  
Protein Interactions ◽  
Regulation Of Gene Expression ◽  
Regulatory Proteins ◽  
Regulatory Sequences ◽  
Protein Protein Interactions ◽  
Cis Acting ◽  
Plant Gene ◽  
Eukaryotic Genes ◽  
Genes Encoding ◽  
Plant Genes

Abstract Over the last decade an intensive research on the regulation of gene expression in viral and animal systems has led to the discovery of cis-acting regulatory sequences, the identification of sequence-specific DNA -binding proteins (trans-acting factors), the characterization of protein domains involved in DNA -protein recognition and binding as well as in protein -protein interactions, and the cloning and sequencing of genes encoding regulatory proteins. The tre­mendous progress in this field is now being complemented by advances in our understanding of how plant genes are regulated. A wealth of data has accumulated in the past few years witnessing basic similarities in the transcriptional regulation of various eukaryotic genes, but also specific features of plant genes. This article collects presently available data, focusses on DNA -protein interactions in plant genes, particularly in light-regulated and “constitutively expressed” genes, reports on the isolation of plant genes encoding regulatory proteins, an dismeant to induce further activities in plant gene research.

scholarly journals Identification of protein-protein and ribonucleoprotein complexes containing Hfq

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Joël Caillet ◽  
Bruno Baron ◽  
Irina V. Boni ◽  
Célia Caillet-Saguy ◽  
Eliane Hajnsdorf
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Direct Interaction ◽  
Rnase A ◽  
Rnase E ◽  
Protein Protein Interactions ◽  
Control Of Gene Expression ◽  
Ribonucleoprotein Complexes

Abstract Hfq is a RNA-binding protein that plays a pivotal role in the control of gene expression in bacteria by stabilizing sRNAs and facilitating their pairing with multiple target mRNAs. It has already been shown that Hfq, directly or indirectly, interacts with many proteins: RNase E, Rho, poly(A)polymerase, RNA polymerase… In order to detect more Hfq-related protein-protein interactions we have used two approaches, TAP-tag combined with RNase A treatment to access the role of RNA in these complexes, and protein-protein crosslinking, which freezes protein-protein complexes formed in vivo. In addition, we have performed microscale thermophoresis to evaluate the role of RNA in some of the complexes detected and used far-western blotting to confirm some protein-protein interactions. Taken together, the results show unambiguously a direct interaction between Hfq and EF-Tu. However a very large number of the interactions of proteins with Hfq in E. coli involve RNAs. These RNAs together with the interacting protein, may play an active role in the formation of Hfq-containing complexes with previously unforeseen implications for the riboregulatory functions of Hfq.

scholarly journals Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure inCaenorhabditis elegans

2019 ◽  
Author(s):  
KM Suen ◽  
F Braukmann ◽  
R Butler ◽  
D Bensaddek ◽  
A Akay ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Direct Interaction ◽  
Specific Protein ◽  
Protein Protein Interactions ◽  
Piwi Domain ◽  
Small Ncrnas ◽  
Complex Forms ◽  
Rna Pathways ◽  
And Function

SummaryMembraneless organelles are platforms for many aspects of RNA biology including small non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise phase separated environments for their function is unclear. To address this question, we investigated how the PIWI-interacting RNA (piRNA) pathway engages with the membraneless organelle P granule inCaenorhabditis elegans. Proteomic analysis of the PIWI protein PRG-1 revealed an interaction with the constitutive P granule protein DEPS-1. Furthermore we identified a novel motif on DEPS-1, PBS, which interacts directly with the Piwi domain of PRG-1. This protein complex forms intertwining ultrastructures to build elongated condensatesin vivo. These sub-organelle ultrastructures depend on the Piwi-interacting motif of DEPS-1 and mediate piRNA function. Additionally, we identify a novel interactor of DEPS-1, EDG-1, which is required for DEPS-1 condensates to form correctly. We show that DEPS-1 is not required for piRNA biogenesis but piRNA function:deps-1mutants fail to produce the secondary endo-siRNAs required for the silencing of piRNA targets. Our study reveals how specific protein-protein interactions drive the spatial organisation and function of small RNA pathways within membraneless organelles.

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